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9vbw

Lectin FRIL from Lablab purpureus complexed to Lewis X tetrasaccharide

Method: X-RAY DIFFRACTION D_max: 178.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vbw
deposition_date	2025-06-05
title	Lectin FRIL from Lablab purpureus complexed to Lewis X tetrasaccharide
keywords	Flt3 receptor-interacting lectin, carbohydrate binding protein, lectin, glycoprotein, complex type glycan, FRIL, PLANT PROTEIN; PLANT PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	55.94 Å
rg_electron	55.48 Å
i0	2485900000.00
molecular_weight	422350.0 kDa
excluded_volume	528640 Å³
envelope_volume	760280 Å³
shell_volume	112050 Å³
envelope_diameter	188.0 Å
shell_rg	60.43 Å
envelope_rg	53.72 Å
shape_rg	55.47 Å
total_rg	55.66 Å
total_atoms	29861
n_residues	3729
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	178.2 Å
rg_real	55.71 Å
rg_real_error	1.91 Å
i0_real	2.4860e+09
i0_real_error	5.7630e+07
rg_reciprocal	56.11 Å
i0_reciprocal	2487000000.0000
total_estimate	0.6523
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	76.4 Å
skewness	0.152
kurtosis	-0.427
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	136100000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 0.999; Sysdev: 0.041; Positv: 1.000; Valcen: 0.967; Smooth: 0.741

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Flt3 receptor-interacting lectin
formula_weight	29075.1 kDa
src_method	nat
entity_count	16

Polymer

type	polypeptide(L)
strand_id	A,E,C,G,I,M,H,D,J,P,L,O,B,F,N,K
atom_count	30738

AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQLTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNANTLNNSSTSENQTTTKAASSNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTTYYPGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTNVAKKENENKYITRGVL

Entity 2 branched

description	alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose
formula_weight	691.6 kDa
src_method	syn
entity_count	16

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	16

Entity 4 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	16

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	858

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6. Citations (1)

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length_a	121.825 Å
length_b	75.237 Å
length_c	241.808 Å
angle_alpha	90.00 °
angle_beta	95.97 °
angle_gamma	90.00 °
z_pdb	32

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.490 Å
resolution_low	29.140 Å
r_factor	0.2072
r_work	0.2066
r_free	0.2463

fit	/app/data/saxs_computation/vb/9vbw/9vbw.fit
pddf	/app/data/pr_computation/vb/9vbw/9vbw.pr.out
profile	/app/data/saxs_computation/vb/9vbw/9vbw.dat

Lectin FRIL from Lablab purpureus complexed to Lewis X tetrasaccharide

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction